Starting phenix.real_space_refine on Tue Aug 26 20:38:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rd4_19065/08_2025/8rd4_19065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rd4_19065/08_2025/8rd4_19065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rd4_19065/08_2025/8rd4_19065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rd4_19065/08_2025/8rd4_19065.map" model { file = "/net/cci-nas-00/data/ceres_data/8rd4_19065/08_2025/8rd4_19065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rd4_19065/08_2025/8rd4_19065.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 1.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 82 5.49 5 S 236 5.16 5 C 25813 2.51 5 N 6925 2.21 5 O 7655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40711 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 28855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3597, 28855 Classifications: {'peptide': 3597} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 155, 'TRANS': 3441} Chain breaks: 19 Chain: "D" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1232 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain breaks: 1 Chain: "E" Number of atoms: 4522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4522 Classifications: {'peptide': 560} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 530} Chain breaks: 1 Chain: "F" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4421 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 26, 'TRANS': 526} Chain: "X" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 842 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "Y" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 839 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Time building chain proxies: 7.74, per 1000 atoms: 0.19 Number of scatterers: 40711 At special positions: 0 Unit cell: (133.48, 167.32, 236.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 236 16.00 P 82 15.00 O 7655 8.00 N 6925 7.00 C 25813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9314 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 15 sheets defined 60.4% alpha, 4.4% beta 33 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 6.20 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.886A pdb=" N ALA A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 removed outlier: 4.147A pdb=" N GLY A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.182A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 4.020A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.644A pdb=" N ILE A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 removed outlier: 3.517A pdb=" N GLY A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 190 removed outlier: 4.216A pdb=" N MET A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.638A pdb=" N GLY A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 228 removed outlier: 4.047A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 4.231A pdb=" N GLU A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.627A pdb=" N HIS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 329 Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.746A pdb=" N LEU A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 removed outlier: 3.670A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 409 through 423 removed outlier: 4.022A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.619A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.864A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASP A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 579 Processing helix chain 'A' and resid 616 through 632 removed outlier: 3.948A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.847A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.544A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 718 Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 744 through 747 Processing helix chain 'A' and resid 748 through 758 removed outlier: 3.567A pdb=" N ALA A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 Processing helix chain 'A' and resid 785 through 789 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.846A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 801 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.944A pdb=" N LYS A 832 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 863 removed outlier: 4.088A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 removed outlier: 4.342A pdb=" N VAL A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.786A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.855A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 4.325A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1003 through 1018 Processing helix chain 'A' and resid 1022 through 1043 removed outlier: 3.826A pdb=" N ARG A1026 " --> pdb=" O ASP A1022 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 3.799A pdb=" N ALA A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1114 removed outlier: 3.861A pdb=" N VAL A1100 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A1103 " --> pdb=" O PHE A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1121 Processing helix chain 'A' and resid 1122 through 1142 removed outlier: 4.040A pdb=" N GLN A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A1127 " --> pdb=" O THR A1123 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.717A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1216 removed outlier: 4.024A pdb=" N GLU A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1222 removed outlier: 3.836A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1217 through 1222' Processing helix chain 'A' and resid 1223 through 1226 Processing helix chain 'A' and resid 1249 through 1272 removed outlier: 3.726A pdb=" N THR A1253 " --> pdb=" O SER A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 3.893A pdb=" N VAL A1281 " --> pdb=" O ALA A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1300 removed outlier: 4.418A pdb=" N PHE A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1298 " --> pdb=" O VAL A1294 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1303 No H-bonds generated for 'chain 'A' and resid 1301 through 1303' Processing helix chain 'A' and resid 1325 through 1352 removed outlier: 3.952A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A1352 " --> pdb=" O LEU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1357 removed outlier: 4.349A pdb=" N LYS A1357 " --> pdb=" O GLU A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1377 Processing helix chain 'A' and resid 1388 through 1393 removed outlier: 3.596A pdb=" N MET A1392 " --> pdb=" O ASP A1388 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1393 " --> pdb=" O VAL A1389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1393' Processing helix chain 'A' and resid 1394 through 1409 removed outlier: 3.827A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A1409 " --> pdb=" O ALA A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1421 Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1444 through 1461 removed outlier: 3.597A pdb=" N LEU A1448 " --> pdb=" O ASP A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1492 removed outlier: 3.893A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A1492 " --> pdb=" O TYR A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1521 Processing helix chain 'A' and resid 1524 through 1534 Processing helix chain 'A' and resid 1557 through 1563 Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.690A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1585 removed outlier: 4.161A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 Processing helix chain 'A' and resid 1613 through 1624 Processing helix chain 'A' and resid 1626 through 1630 Processing helix chain 'A' and resid 1641 through 1654 Processing helix chain 'A' and resid 1667 through 1679 Processing helix chain 'A' and resid 1685 through 1693 removed outlier: 4.379A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1700 Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1705 through 1721 Processing helix chain 'A' and resid 1733 through 1753 removed outlier: 3.738A pdb=" N SER A1753 " --> pdb=" O ALA A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.545A pdb=" N LEU A1761 " --> pdb=" O MET A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1786 Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.571A pdb=" N VAL A1795 " --> pdb=" O CYS A1791 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1822 removed outlier: 4.120A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1831 removed outlier: 3.757A pdb=" N CYS A1831 " --> pdb=" O LEU A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1835 No H-bonds generated for 'chain 'A' and resid 1833 through 1835' Processing helix chain 'A' and resid 1836 through 1842 Processing helix chain 'A' and resid 1843 through 1853 removed outlier: 3.723A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1884 removed outlier: 4.473A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1894 through 1899 Processing helix chain 'A' and resid 1911 through 1922 removed outlier: 3.679A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1955 Processing helix chain 'A' and resid 1970 through 1974 Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.903A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A1982 " --> pdb=" O PHE A1978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1977 through 1982' Processing helix chain 'A' and resid 2087 through 2091 Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2127 through 2135 removed outlier: 3.705A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.763A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.892A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2164 through 2174 Processing helix chain 'A' and resid 2182 through 2194 Processing helix chain 'A' and resid 2195 through 2197 No H-bonds generated for 'chain 'A' and resid 2195 through 2197' Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2252 through 2261 Processing helix chain 'A' and resid 2268 through 2283 removed outlier: 4.213A pdb=" N VAL A2272 " --> pdb=" O LYS A2268 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.162A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2351 removed outlier: 3.828A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.772A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2418 removed outlier: 3.834A pdb=" N GLN A2414 " --> pdb=" O GLU A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2426 removed outlier: 3.598A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A2426 " --> pdb=" O GLN A2422 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2460 removed outlier: 3.601A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 3.621A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2484 removed outlier: 3.844A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A2484 " --> pdb=" O ILE A2480 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 removed outlier: 3.982A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A2500 " --> pdb=" O GLN A2496 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2527 Processing helix chain 'A' and resid 2534 through 2543 removed outlier: 3.962A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 3.910A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2566 through 2568 No H-bonds generated for 'chain 'A' and resid 2566 through 2568' Processing helix chain 'A' and resid 2787 through 2799 removed outlier: 3.591A pdb=" N THR A2792 " --> pdb=" O SER A2788 " (cutoff:3.500A) Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2821 removed outlier: 3.763A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 3.560A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2864 Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2897 removed outlier: 3.796A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2933 removed outlier: 3.591A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.608A pdb=" N THR A2944 " --> pdb=" O ARG A2940 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A2946 " --> pdb=" O ILE A2942 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2962 removed outlier: 3.532A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2966 through 2977 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3017 removed outlier: 3.609A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3034 through 3055 removed outlier: 3.864A pdb=" N LEU A3041 " --> pdb=" O GLN A3037 " (cutoff:3.500A) Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3060 through 3069 removed outlier: 3.538A pdb=" N PHE A3064 " --> pdb=" O SER A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3075 through 3081 removed outlier: 4.005A pdb=" N HIS A3081 " --> pdb=" O ILE A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3093 Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 3.651A pdb=" N ALA A3099 " --> pdb=" O ASP A3095 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3130 Processing helix chain 'A' and resid 3131 through 3147 Processing helix chain 'A' and resid 3147 through 3152 removed outlier: 3.967A pdb=" N LEU A3151 " --> pdb=" O LYS A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3194 removed outlier: 3.692A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3230 through 3249 Processing helix chain 'A' and resid 3253 through 3263 removed outlier: 3.614A pdb=" N GLU A3261 " --> pdb=" O LYS A3257 " (cutoff:3.500A) Processing helix chain 'A' and resid 3264 through 3267 removed outlier: 4.013A pdb=" N LYS A3267 " --> pdb=" O LYS A3264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3264 through 3267' Processing helix chain 'A' and resid 3272 through 3290 removed outlier: 3.878A pdb=" N SER A3290 " --> pdb=" O CYS A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3292 through 3299 removed outlier: 3.877A pdb=" N VAL A3297 " --> pdb=" O CYS A3293 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A3298 " --> pdb=" O SER A3294 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3309 Processing helix chain 'A' and resid 3314 through 3318 removed outlier: 3.644A pdb=" N LYS A3318 " --> pdb=" O TYR A3315 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3344 removed outlier: 3.798A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3352 through 3360 Processing helix chain 'A' and resid 3371 through 3391 removed outlier: 3.853A pdb=" N ALA A3391 " --> pdb=" O GLU A3387 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3428 removed outlier: 3.872A pdb=" N GLU A3427 " --> pdb=" O GLN A3423 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A3428 " --> pdb=" O LEU A3424 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3457 removed outlier: 3.656A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A3457 " --> pdb=" O ALA A3453 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3465 through 3475 removed outlier: 3.787A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) Processing helix chain 'A' and resid 3479 through 3487 Processing helix chain 'A' and resid 3491 through 3497 removed outlier: 3.722A pdb=" N GLN A3494 " --> pdb=" O PRO A3491 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A3496 " --> pdb=" O TRP A3493 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER A3497 " --> pdb=" O GLN A3494 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3506 removed outlier: 3.631A pdb=" N MET A3502 " --> pdb=" O TRP A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3510 through 3514 Processing helix chain 'A' and resid 3515 through 3525 Processing helix chain 'A' and resid 3529 through 3539 removed outlier: 4.228A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3550 Processing helix chain 'A' and resid 3551 through 3562 Processing helix chain 'A' and resid 3567 through 3579 removed outlier: 3.719A pdb=" N LEU A3578 " --> pdb=" O ALA A3574 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A3579 " --> pdb=" O LEU A3575 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3599 removed outlier: 3.863A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A3597 " --> pdb=" O ARG A3593 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3615 Processing helix chain 'A' and resid 3632 through 3640 Processing helix chain 'A' and resid 3644 through 3649 Processing helix chain 'A' and resid 3660 through 3662 No H-bonds generated for 'chain 'A' and resid 3660 through 3662' Processing helix chain 'A' and resid 3663 through 3672 removed outlier: 3.545A pdb=" N LEU A3667 " --> pdb=" O THR A3663 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3683 removed outlier: 3.843A pdb=" N CYS A3683 " --> pdb=" O LEU A3680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3680 through 3683' Processing helix chain 'A' and resid 3684 through 3689 Processing helix chain 'A' and resid 3758 through 3776 Processing helix chain 'A' and resid 3778 through 3784 removed outlier: 4.220A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.704A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3848 Processing helix chain 'A' and resid 3854 through 3859 Processing helix chain 'A' and resid 3860 through 3862 No H-bonds generated for 'chain 'A' and resid 3860 through 3862' Processing helix chain 'A' and resid 3863 through 3876 Processing helix chain 'A' and resid 3881 through 3889 Processing helix chain 'A' and resid 3896 through 3918 removed outlier: 3.762A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3970 through 3972 No H-bonds generated for 'chain 'A' and resid 3970 through 3972' Processing helix chain 'A' and resid 3979 through 3994 removed outlier: 3.661A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3996 through 4007 Processing helix chain 'A' and resid 4015 through 4022 Processing helix chain 'A' and resid 4032 through 4039 removed outlier: 3.700A pdb=" N TRP A4038 " --> pdb=" O GLU A4035 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A4039 " --> pdb=" O LYS A4036 " (cutoff:3.500A) Processing helix chain 'A' and resid 4041 through 4053 removed outlier: 3.783A pdb=" N CYS A4045 " --> pdb=" O ARG A4041 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 removed outlier: 3.669A pdb=" N GLY A4083 " --> pdb=" O ALA A4079 " (cutoff:3.500A) Processing helix chain 'A' and resid 4088 through 4092 Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4119 removed outlier: 3.704A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4120 through 4125 removed outlier: 6.141A pdb=" N GLY A4123 " --> pdb=" O THR A4120 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 removed outlier: 3.788A pdb=" N ARG D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR D 44 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.715A pdb=" N ARG D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.801A pdb=" N ASP D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 58 through 77 removed outlier: 3.532A pdb=" N ILE E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 119 through 122 Processing helix chain 'E' and resid 123 through 135 Processing helix chain 'E' and resid 144 through 156 Processing helix chain 'E' and resid 179 through 197 removed outlier: 3.600A pdb=" N ALA E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.553A pdb=" N GLU E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 356 No H-bonds generated for 'chain 'E' and resid 354 through 356' Processing helix chain 'E' and resid 377 through 392 removed outlier: 3.761A pdb=" N LEU E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.507A pdb=" N LYS E 443 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'E' and resid 480 through 495 Processing helix chain 'E' and resid 510 through 519 Processing helix chain 'E' and resid 520 through 530 Processing helix chain 'E' and resid 560 through 571 removed outlier: 3.741A pdb=" N LEU E 564 " --> pdb=" O SER E 560 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 589 Processing helix chain 'E' and resid 595 through 609 removed outlier: 3.852A pdb=" N LEU E 599 " --> pdb=" O LYS E 595 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 604 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN E 608 " --> pdb=" O THR E 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 Processing helix chain 'F' and resid 29 through 48 Processing helix chain 'F' and resid 87 through 95 removed outlier: 3.849A pdb=" N LEU F 91 " --> pdb=" O ASP F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 122 removed outlier: 3.518A pdb=" N ALA F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 216 Processing helix chain 'F' and resid 217 through 224 removed outlier: 3.596A pdb=" N ASP F 222 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE F 224 " --> pdb=" O LEU F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.670A pdb=" N LEU F 231 " --> pdb=" O PHE F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 231' Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 324 through 331 Processing helix chain 'F' and resid 372 through 387 removed outlier: 3.796A pdb=" N ALA F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 461 Processing helix chain 'F' and resid 466 through 470 removed outlier: 3.858A pdb=" N THR F 470 " --> pdb=" O ASP F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 500 removed outlier: 3.939A pdb=" N GLN F 488 " --> pdb=" O ASN F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 516 Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 526 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA2, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.520A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3741 through 3742 removed outlier: 3.869A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3810 through 3811 Processing sheet with id=AA5, first strand: chain 'D' and resid 52 through 54 removed outlier: 6.617A pdb=" N PHE D 31 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 63 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 102 through 104 removed outlier: 3.704A pdb=" N VAL E 42 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG E 35 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS E 163 " --> pdb=" O ARG E 35 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 165 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N PHE E 199 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS E 164 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASP E 201 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE E 166 " --> pdb=" O ASP E 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 258 through 262 removed outlier: 7.773A pdb=" N VAL E 394 " --> pdb=" O PRO E 415 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA E 395 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE E 350 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU E 397 " --> pdb=" O MET E 348 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 401 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU E 345 " --> pdb=" O ARG E 258 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS E 260 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 347 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS E 262 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY E 349 " --> pdb=" O LYS E 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 288 through 289 Processing sheet with id=AA9, first strand: chain 'E' and resid 300 through 303 removed outlier: 4.088A pdb=" N ARG E 301 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU F 292 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN F 290 " --> pdb=" O PHE E 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 325 through 329 Processing sheet with id=AB2, first strand: chain 'E' and resid 419 through 420 removed outlier: 6.754A pdb=" N GLU E 419 " --> pdb=" O VAL E 427 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 81 through 84 removed outlier: 4.499A pdb=" N LEU F 83 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE F 54 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 15 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N GLN F 162 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE F 132 " --> pdb=" O GLN F 162 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE F 164 " --> pdb=" O ILE F 132 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE F 134 " --> pdb=" O PHE F 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 248 through 253 removed outlier: 3.557A pdb=" N LEU F 257 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL F 361 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU F 268 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN F 359 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLN F 360 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLN F 423 " --> pdb=" O GLN F 360 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA F 391 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY F 344 " --> pdb=" O ILE F 392 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG F 394 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL F 342 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA F 396 " --> pdb=" O PHE F 340 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE F 340 " --> pdb=" O ALA F 396 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N PHE F 340 " --> pdb=" O PRO F 248 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG F 250 " --> pdb=" O PHE F 340 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL F 342 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR F 252 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 344 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 314 through 316 removed outlier: 3.906A pdb=" N ASP F 319 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 464 through 465 1862 hydrogen bonds defined for protein. 5379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 12.39 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11161 1.33 - 1.46: 7451 1.46 - 1.58: 22559 1.58 - 1.70: 164 1.70 - 1.82: 373 Bond restraints: 41708 Sorted by residual: bond pdb=" N GLN A1231 " pdb=" CA GLN A1231 " ideal model delta sigma weight residual 1.453 1.535 -0.082 2.23e-02 2.01e+03 1.36e+01 bond pdb=" CB PRO A1734 " pdb=" CG PRO A1734 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.57e+00 bond pdb=" N ASN E 535 " pdb=" CA ASN E 535 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.64e-02 3.72e+03 4.44e+00 bond pdb=" N MET A2568 " pdb=" CA MET A2568 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.32e+00 bond pdb=" CB PRO A1991 " pdb=" CG PRO A1991 " ideal model delta sigma weight residual 1.492 1.596 -0.104 5.00e-02 4.00e+02 4.29e+00 ... (remaining 41703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 56169 3.00 - 6.01: 435 6.01 - 9.01: 49 9.01 - 12.02: 11 12.02 - 15.02: 4 Bond angle restraints: 56668 Sorted by residual: angle pdb=" CA PRO A1734 " pdb=" N PRO A1734 " pdb=" CD PRO A1734 " ideal model delta sigma weight residual 112.00 99.95 12.05 1.40e+00 5.10e-01 7.41e+01 angle pdb=" CA PRO A1991 " pdb=" N PRO A1991 " pdb=" CD PRO A1991 " ideal model delta sigma weight residual 112.00 103.52 8.48 1.40e+00 5.10e-01 3.67e+01 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 112.96 108.10 4.86 1.00e+00 1.00e+00 2.37e+01 angle pdb=" N TRP D 164 " pdb=" CA TRP D 164 " pdb=" C TRP D 164 " ideal model delta sigma weight residual 112.88 106.95 5.93 1.29e+00 6.01e-01 2.11e+01 angle pdb=" CA GLN A2291 " pdb=" CB GLN A2291 " pdb=" CG GLN A2291 " ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 ... (remaining 56663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 23890 34.97 - 69.94: 1343 69.94 - 104.92: 60 104.92 - 139.89: 2 139.89 - 174.86: 3 Dihedral angle restraints: 25298 sinusoidal: 10996 harmonic: 14302 Sorted by residual: dihedral pdb=" CA ARG D 183 " pdb=" C ARG D 183 " pdb=" N TYR D 184 " pdb=" CA TYR D 184 " ideal model delta harmonic sigma weight residual 180.00 129.77 50.23 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA LEU A2249 " pdb=" C LEU A2249 " pdb=" N SER A2250 " pdb=" CA SER A2250 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ILE D 134 " pdb=" C ILE D 134 " pdb=" N ALA D 135 " pdb=" CA ALA D 135 " ideal model delta harmonic sigma weight residual 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 25295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5604 0.063 - 0.125: 746 0.125 - 0.188: 35 0.188 - 0.251: 4 0.251 - 0.313: 1 Chirality restraints: 6390 Sorted by residual: chirality pdb=" CG LEU A 272 " pdb=" CB LEU A 272 " pdb=" CD1 LEU A 272 " pdb=" CD2 LEU A 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE A2251 " pdb=" N ILE A2251 " pdb=" C ILE A2251 " pdb=" CB ILE A2251 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A3739 " pdb=" CA ILE A3739 " pdb=" CG1 ILE A3739 " pdb=" CG2 ILE A3739 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 6387 not shown) Planarity restraints: 6926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1990 " 0.093 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO A1991 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A1991 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A1991 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 312 " 0.089 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO E 313 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO E 313 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 313 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1733 " -0.090 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A1734 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO A1734 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A1734 " -0.066 5.00e-02 4.00e+02 ... (remaining 6923 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1547 2.71 - 3.26: 42285 3.26 - 3.80: 66730 3.80 - 4.35: 80062 4.35 - 4.90: 132030 Nonbonded interactions: 322654 Sorted by model distance: nonbonded pdb=" OH TYR E 369 " pdb=" O SER F 436 " model vdw 2.159 3.040 nonbonded pdb=" O PHE A1219 " pdb=" OG1 THR A1223 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A1045 " pdb=" OE1 GLN A1047 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR E 588 " pdb=" NE2 HIS E 606 " model vdw 2.179 3.120 nonbonded pdb=" O HIS A 533 " pdb=" OG SER A 537 " model vdw 2.186 3.040 ... (remaining 322649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 40.610 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 41708 Z= 0.161 Angle : 0.692 15.023 56668 Z= 0.356 Chirality : 0.041 0.313 6390 Planarity : 0.005 0.135 6926 Dihedral : 19.559 174.859 15984 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.11 % Favored : 89.87 % Rotamer: Outliers : 0.51 % Allowed : 32.02 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.13), residues: 4818 helix: 0.89 (0.11), residues: 2588 sheet: -1.41 (0.36), residues: 209 loop : -2.13 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3612 TYR 0.017 0.001 TYR F 395 PHE 0.031 0.001 PHE A2577 TRP 0.023 0.001 TRP D 177 HIS 0.008 0.001 HIS A3643 Details of bonding type rmsd covalent geometry : bond 0.00377 (41708) covalent geometry : angle 0.69231 (56668) hydrogen bonds : bond 0.15275 ( 1943) hydrogen bonds : angle 5.82140 ( 5541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 494 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7471 (t80) REVERT: A 1269 THR cc_start: 0.8979 (t) cc_final: 0.8718 (t) REVERT: A 1724 MET cc_start: 0.6803 (mmm) cc_final: 0.6551 (mtp) REVERT: A 3414 MET cc_start: 0.8022 (mmm) cc_final: 0.7643 (mmm) REVERT: A 4109 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7642 (t0) REVERT: F 183 PHE cc_start: 0.6885 (t80) cc_final: 0.6667 (t80) REVERT: F 357 MET cc_start: 0.8142 (mmm) cc_final: 0.7661 (mmm) outliers start: 22 outliers final: 9 residues processed: 511 average time/residue: 0.2149 time to fit residues: 185.7076 Evaluate side-chains 481 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 470 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 2283 ASN Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 261 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 484 HIS A 539 GLN A1083 ASN A1325 GLN A1901 HIS A2152 ASN A2795 GLN A2859 GLN A3003 ASN A3470 GLN A3634 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.139071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102076 restraints weight = 86600.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103805 restraints weight = 43691.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104347 restraints weight = 29822.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104840 restraints weight = 28481.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104851 restraints weight = 24199.294| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 41708 Z= 0.143 Angle : 0.639 10.710 56668 Z= 0.329 Chirality : 0.041 0.266 6390 Planarity : 0.005 0.079 6926 Dihedral : 14.378 175.905 6153 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.90 % Allowed : 28.89 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.13), residues: 4818 helix: 0.87 (0.11), residues: 2651 sheet: -1.34 (0.35), residues: 216 loop : -2.20 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3612 TYR 0.015 0.001 TYR E 534 PHE 0.031 0.001 PHE F 477 TRP 0.013 0.001 TRP A3916 HIS 0.005 0.001 HIS F 511 Details of bonding type rmsd covalent geometry : bond 0.00327 (41708) covalent geometry : angle 0.63856 (56668) hydrogen bonds : bond 0.03910 ( 1943) hydrogen bonds : angle 4.59571 ( 5541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 529 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.2157 (OUTLIER) cc_final: 0.0864 (mmp-170) REVERT: A 441 MET cc_start: 0.7908 (tpp) cc_final: 0.7341 (tpp) REVERT: A 707 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7698 (t80) REVERT: A 734 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8837 (mm) REVERT: A 1269 THR cc_start: 0.9214 (t) cc_final: 0.8901 (t) REVERT: A 1408 MET cc_start: 0.8372 (mmm) cc_final: 0.8139 (mmm) REVERT: A 1751 GLU cc_start: 0.7729 (pt0) cc_final: 0.7507 (pt0) REVERT: A 1880 MET cc_start: 0.8305 (mmm) cc_final: 0.8061 (mmt) REVERT: A 1906 THR cc_start: 0.4802 (OUTLIER) cc_final: 0.4347 (m) REVERT: A 1946 ASN cc_start: 0.9429 (m-40) cc_final: 0.8899 (m110) REVERT: A 3613 MET cc_start: 0.9115 (tmm) cc_final: 0.8741 (ttp) REVERT: A 3694 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: A 3933 GLU cc_start: 0.8113 (tt0) cc_final: 0.7831 (tp30) REVERT: A 4109 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7839 (t0) REVERT: E 129 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8586 (ttpp) REVERT: E 167 MET cc_start: 0.8152 (mpp) cc_final: 0.7915 (mpp) REVERT: F 103 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: F 357 MET cc_start: 0.7929 (mmm) cc_final: 0.7368 (mmm) outliers start: 170 outliers final: 69 residues processed: 666 average time/residue: 0.2234 time to fit residues: 252.6217 Evaluate side-chains 563 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 486 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1629 CYS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1856 THR Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1886 LYS Chi-restraints excluded: chain A residue 1906 THR Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 2972 TYR Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4116 ILE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 314 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 404 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 380 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 220 optimal weight: 0.0020 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 191 ASN ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN A2859 GLN A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.139275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102808 restraints weight = 86435.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103433 restraints weight = 45990.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104765 restraints weight = 30199.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105264 restraints weight = 27428.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.105180 restraints weight = 23974.787| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41708 Z= 0.138 Angle : 0.628 10.318 56668 Z= 0.321 Chirality : 0.041 0.247 6390 Planarity : 0.004 0.075 6926 Dihedral : 14.331 176.488 6145 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.94 % Favored : 90.04 % Rotamer: Outliers : 4.09 % Allowed : 28.50 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.13), residues: 4818 helix: 0.88 (0.11), residues: 2663 sheet: -1.39 (0.36), residues: 204 loop : -2.22 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3746 TYR 0.021 0.001 TYR E 534 PHE 0.028 0.001 PHE F 477 TRP 0.030 0.001 TRP A2245 HIS 0.005 0.001 HIS F 188 Details of bonding type rmsd covalent geometry : bond 0.00314 (41708) covalent geometry : angle 0.62772 (56668) hydrogen bonds : bond 0.03543 ( 1943) hydrogen bonds : angle 4.41122 ( 5541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 536 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.7934 (tpp) cc_final: 0.7368 (tpp) REVERT: A 707 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 734 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 831 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 1269 THR cc_start: 0.9212 (t) cc_final: 0.8900 (t) REVERT: A 1325 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8369 (pp30) REVERT: A 1670 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8306 (mp0) REVERT: A 1751 GLU cc_start: 0.7797 (pt0) cc_final: 0.7495 (pt0) REVERT: A 1873 TYR cc_start: 0.8698 (m-80) cc_final: 0.8026 (m-80) REVERT: A 1880 MET cc_start: 0.8397 (mmm) cc_final: 0.8197 (mmt) REVERT: A 1946 ASN cc_start: 0.9416 (m-40) cc_final: 0.8930 (m110) REVERT: A 2860 ASP cc_start: 0.8413 (t0) cc_final: 0.8131 (t0) REVERT: A 3115 SER cc_start: 0.9280 (m) cc_final: 0.8987 (p) REVERT: A 3232 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6785 (tmm-80) REVERT: A 3423 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8542 (mm-40) REVERT: A 3540 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.5722 (t80) REVERT: A 3590 ASN cc_start: 0.8980 (m-40) cc_final: 0.8749 (m-40) REVERT: A 3613 MET cc_start: 0.9104 (tmm) cc_final: 0.8677 (ttp) REVERT: A 3694 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: A 3856 MET cc_start: 0.7669 (tpt) cc_final: 0.7450 (tpt) REVERT: A 3933 GLU cc_start: 0.8166 (tt0) cc_final: 0.7737 (tp30) REVERT: A 4109 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7863 (t0) REVERT: D 69 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: E 129 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8584 (ttpp) REVERT: F 53 GLU cc_start: 0.7485 (mp0) cc_final: 0.7186 (mm-30) REVERT: F 103 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8113 (mm-40) REVERT: F 306 LEU cc_start: 0.9042 (mm) cc_final: 0.8835 (mt) outliers start: 178 outliers final: 96 residues processed: 682 average time/residue: 0.2164 time to fit residues: 252.1675 Evaluate side-chains 587 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 479 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1325 GLN Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1829 TRP Chi-restraints excluded: chain A residue 1856 THR Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3191 SER Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3423 GLN Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3668 LEU Chi-restraints excluded: chain A residue 3670 MET Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3930 VAL Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 171 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 317 optimal weight: 0.0020 chunk 298 optimal weight: 7.9990 chunk 329 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 356 optimal weight: 0.4980 chunk 234 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2859 GLN A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102713 restraints weight = 85911.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104834 restraints weight = 41253.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.105051 restraints weight = 27973.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105521 restraints weight = 26565.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105616 restraints weight = 23434.613| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41708 Z= 0.133 Angle : 0.630 13.390 56668 Z= 0.320 Chirality : 0.040 0.218 6390 Planarity : 0.004 0.074 6926 Dihedral : 14.290 176.144 6143 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 4.48 % Allowed : 28.07 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.13), residues: 4818 helix: 0.91 (0.11), residues: 2662 sheet: -1.31 (0.36), residues: 206 loop : -2.23 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2228 TYR 0.015 0.001 TYR F 395 PHE 0.027 0.001 PHE F 477 TRP 0.012 0.001 TRP A3916 HIS 0.005 0.001 HIS F 188 Details of bonding type rmsd covalent geometry : bond 0.00305 (41708) covalent geometry : angle 0.62957 (56668) hydrogen bonds : bond 0.03330 ( 1943) hydrogen bonds : angle 4.31686 ( 5541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 521 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8776 (t) REVERT: A 441 MET cc_start: 0.7897 (tpp) cc_final: 0.7338 (tpp) REVERT: A 707 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7749 (t80) REVERT: A 734 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 831 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8749 (mm) REVERT: A 1269 THR cc_start: 0.9210 (t) cc_final: 0.8899 (t) REVERT: A 1648 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 1667 SER cc_start: 0.8214 (t) cc_final: 0.7680 (p) REVERT: A 1751 GLU cc_start: 0.7832 (pt0) cc_final: 0.7479 (pt0) REVERT: A 1873 TYR cc_start: 0.8663 (m-80) cc_final: 0.8037 (m-80) REVERT: A 1946 ASN cc_start: 0.9374 (m-40) cc_final: 0.8890 (m110) REVERT: A 1990 PHE cc_start: 0.5581 (m-80) cc_final: 0.5004 (m-10) REVERT: A 2236 GLU cc_start: 0.9047 (tt0) cc_final: 0.8443 (tp30) REVERT: A 2860 ASP cc_start: 0.8430 (t0) cc_final: 0.8178 (t0) REVERT: A 3232 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6787 (tmm-80) REVERT: A 3418 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8802 (p0) REVERT: A 3540 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.5748 (t80) REVERT: A 3590 ASN cc_start: 0.8983 (m-40) cc_final: 0.8777 (m-40) REVERT: A 3610 TYR cc_start: 0.7954 (t80) cc_final: 0.7701 (t80) REVERT: A 3613 MET cc_start: 0.9127 (tmm) cc_final: 0.8637 (ttp) REVERT: A 3856 MET cc_start: 0.7797 (tpt) cc_final: 0.7547 (tpt) REVERT: A 3933 GLU cc_start: 0.8179 (tt0) cc_final: 0.7714 (tp30) REVERT: A 4109 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.7849 (t0) REVERT: D 34 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7733 (ptp90) REVERT: D 69 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: E 167 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: E 409 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.6705 (t80) REVERT: E 498 MET cc_start: 0.8076 (tpp) cc_final: 0.7854 (tpp) REVERT: F 103 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8118 (mm-40) REVERT: F 126 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7378 (mmtm) REVERT: F 223 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: F 461 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8424 (mtm) outliers start: 195 outliers final: 114 residues processed: 669 average time/residue: 0.2195 time to fit residues: 249.8416 Evaluate side-chains 624 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 493 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2942 ILE Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3670 MET Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 229 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 478 optimal weight: 0.7980 chunk 337 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 326 optimal weight: 0.9980 chunk 151 optimal weight: 0.3980 chunk 242 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 0.5980 chunk 419 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 192 ASN A1325 GLN A1442 GLN A2859 GLN A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.137559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102050 restraints weight = 83238.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103695 restraints weight = 42724.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103692 restraints weight = 31019.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104160 restraints weight = 30933.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104318 restraints weight = 26589.459| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41708 Z= 0.121 Angle : 0.629 12.304 56668 Z= 0.316 Chirality : 0.040 0.224 6390 Planarity : 0.004 0.081 6926 Dihedral : 14.247 175.923 6143 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.63 % Favored : 90.35 % Rotamer: Outliers : 4.59 % Allowed : 28.50 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 4818 helix: 0.94 (0.11), residues: 2660 sheet: -1.24 (0.37), residues: 204 loop : -2.20 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.014 0.001 TYR F 395 PHE 0.030 0.001 PHE A1296 TRP 0.012 0.001 TRP A3916 HIS 0.005 0.001 HIS F 188 Details of bonding type rmsd covalent geometry : bond 0.00275 (41708) covalent geometry : angle 0.62884 (56668) hydrogen bonds : bond 0.03150 ( 1943) hydrogen bonds : angle 4.23086 ( 5541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 541 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 734 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8854 (mm) REVERT: A 831 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 1269 THR cc_start: 0.9201 (t) cc_final: 0.8989 (t) REVERT: A 1561 SER cc_start: 0.8604 (m) cc_final: 0.8358 (p) REVERT: A 1648 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8219 (tt) REVERT: A 1751 GLU cc_start: 0.7844 (pt0) cc_final: 0.7457 (pt0) REVERT: A 1873 TYR cc_start: 0.8571 (m-80) cc_final: 0.8066 (m-80) REVERT: A 1946 ASN cc_start: 0.9298 (m-40) cc_final: 0.8766 (m110) REVERT: A 1990 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4931 (m-80) REVERT: A 2236 GLU cc_start: 0.8908 (tt0) cc_final: 0.8382 (tp30) REVERT: A 2568 MET cc_start: 0.8267 (ppp) cc_final: 0.8012 (ppp) REVERT: A 2860 ASP cc_start: 0.8409 (t0) cc_final: 0.8080 (t0) REVERT: A 3135 LEU cc_start: 0.9203 (mm) cc_final: 0.8985 (mt) REVERT: A 3418 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8750 (p0) REVERT: A 3540 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5737 (t80) REVERT: A 3613 MET cc_start: 0.9037 (tmm) cc_final: 0.8529 (ttp) REVERT: A 3856 MET cc_start: 0.7786 (tpt) cc_final: 0.7523 (tpt) REVERT: A 3933 GLU cc_start: 0.8129 (tt0) cc_final: 0.7643 (tp30) REVERT: A 4109 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7872 (t0) REVERT: A 4122 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: D 69 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: E 129 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8566 (ttpp) REVERT: E 135 MET cc_start: 0.8814 (mmt) cc_final: 0.8279 (mmt) REVERT: E 167 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: E 409 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.6582 (t80) REVERT: F 461 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8477 (mtm) outliers start: 200 outliers final: 115 residues processed: 693 average time/residue: 0.2129 time to fit residues: 251.6347 Evaluate side-chains 627 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 498 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1202 ARG Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1990 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2408 MET Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3191 SER Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3410 ILE Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3456 LEU Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3670 MET Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3955 VAL Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 536 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 484 optimal weight: 3.9990 chunk 385 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 486 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1084 ASN A1325 GLN A1859 ASN A1890 HIS A2859 GLN A2977 ASN A3602 ASN A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.136896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099026 restraints weight = 83834.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100656 restraints weight = 43925.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101380 restraints weight = 30067.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101975 restraints weight = 26713.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102075 restraints weight = 24277.758| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41708 Z= 0.142 Angle : 0.642 13.154 56668 Z= 0.322 Chirality : 0.041 0.226 6390 Planarity : 0.004 0.073 6926 Dihedral : 14.265 176.105 6143 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.57 % Favored : 90.39 % Rotamer: Outliers : 4.98 % Allowed : 28.14 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 4818 helix: 0.96 (0.11), residues: 2660 sheet: -1.31 (0.36), residues: 206 loop : -2.20 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 782 TYR 0.015 0.001 TYR F 416 PHE 0.028 0.001 PHE A2577 TRP 0.022 0.001 TRP A2981 HIS 0.006 0.001 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00331 (41708) covalent geometry : angle 0.64221 (56668) hydrogen bonds : bond 0.03204 ( 1943) hydrogen bonds : angle 4.24327 ( 5541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 512 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.1938 (OUTLIER) cc_final: 0.0610 (mmp-170) REVERT: A 441 MET cc_start: 0.7878 (tpp) cc_final: 0.7308 (tpp) REVERT: A 707 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 734 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 831 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8704 (mm) REVERT: A 1269 THR cc_start: 0.9199 (t) cc_final: 0.8918 (t) REVERT: A 1428 ILE cc_start: 0.9306 (mm) cc_final: 0.9046 (mm) REVERT: A 1648 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8194 (tt) REVERT: A 1711 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7923 (ttm-80) REVERT: A 1873 TYR cc_start: 0.8663 (m-80) cc_final: 0.8084 (m-80) REVERT: A 1946 ASN cc_start: 0.9389 (m-40) cc_final: 0.8850 (m110) REVERT: A 1990 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: A 2568 MET cc_start: 0.8334 (ppp) cc_final: 0.7953 (ppp) REVERT: A 2860 ASP cc_start: 0.8452 (t0) cc_final: 0.8108 (t0) REVERT: A 3232 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6737 (tmm-80) REVERT: A 3414 MET cc_start: 0.8210 (mmm) cc_final: 0.7931 (mmm) REVERT: A 3418 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8786 (p0) REVERT: A 3540 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5720 (t80) REVERT: A 3613 MET cc_start: 0.9142 (tmm) cc_final: 0.8748 (ttp) REVERT: A 3856 MET cc_start: 0.7826 (tpt) cc_final: 0.7553 (tpt) REVERT: A 3933 GLU cc_start: 0.8173 (tt0) cc_final: 0.7665 (tp30) REVERT: A 4109 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7879 (t0) REVERT: A 4122 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8808 (pt0) REVERT: D 34 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7745 (ptp90) REVERT: D 69 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: E 129 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8595 (ttpp) REVERT: E 167 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7362 (mpt) REVERT: E 409 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.6769 (t80) REVERT: F 126 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6897 (tptt) REVERT: F 223 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: F 225 TYR cc_start: 0.8057 (m-80) cc_final: 0.7482 (m-80) REVERT: F 357 MET cc_start: 0.7799 (mmm) cc_final: 0.7429 (mmm) REVERT: F 461 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8452 (mtm) outliers start: 217 outliers final: 141 residues processed: 678 average time/residue: 0.2266 time to fit residues: 263.1990 Evaluate side-chains 645 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 484 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1356 TRP Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1711 ARG Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1990 PHE Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2408 MET Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2486 ASP Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3191 SER Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3456 LEU Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3614 TYR Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4116 ILE Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 607 PHE Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 25 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 313 optimal weight: 0.8980 chunk 449 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 483 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1084 ASN A1325 GLN A2859 GLN A2977 ASN A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.137681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100522 restraints weight = 83778.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101946 restraints weight = 46009.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102144 restraints weight = 31628.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102787 restraints weight = 31016.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102970 restraints weight = 26898.601| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41708 Z= 0.126 Angle : 0.652 14.465 56668 Z= 0.324 Chirality : 0.041 0.190 6390 Planarity : 0.004 0.072 6926 Dihedral : 14.242 175.883 6143 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.42 % Favored : 90.54 % Rotamer: Outliers : 4.64 % Allowed : 28.66 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.13), residues: 4818 helix: 0.98 (0.11), residues: 2654 sheet: -1.30 (0.37), residues: 201 loop : -2.16 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A3612 TYR 0.014 0.001 TYR F 395 PHE 0.030 0.001 PHE A2577 TRP 0.013 0.001 TRP A2981 HIS 0.005 0.001 HIS F 188 Details of bonding type rmsd covalent geometry : bond 0.00289 (41708) covalent geometry : angle 0.65248 (56668) hydrogen bonds : bond 0.03113 ( 1943) hydrogen bonds : angle 4.20077 ( 5541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 518 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.1950 (OUTLIER) cc_final: 0.0640 (mmp-170) REVERT: A 157 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.5558 (p90) REVERT: A 326 MET cc_start: 0.9105 (mpp) cc_final: 0.8728 (mpp) REVERT: A 441 MET cc_start: 0.7860 (tpp) cc_final: 0.7305 (tpp) REVERT: A 707 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 734 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 831 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8678 (mm) REVERT: A 1255 CYS cc_start: 0.8177 (m) cc_final: 0.7837 (m) REVERT: A 1269 THR cc_start: 0.9152 (t) cc_final: 0.8936 (t) REVERT: A 1561 SER cc_start: 0.8609 (m) cc_final: 0.8397 (p) REVERT: A 1648 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 1711 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: A 1724 MET cc_start: 0.7643 (mmm) cc_final: 0.6932 (mtp) REVERT: A 1873 TYR cc_start: 0.8645 (m-80) cc_final: 0.8105 (m-80) REVERT: A 1946 ASN cc_start: 0.9386 (m-40) cc_final: 0.8842 (m110) REVERT: A 2568 MET cc_start: 0.8330 (ppp) cc_final: 0.7773 (ppp) REVERT: A 2860 ASP cc_start: 0.8446 (t0) cc_final: 0.8079 (t0) REVERT: A 3232 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6738 (tmm-80) REVERT: A 3414 MET cc_start: 0.8219 (mmm) cc_final: 0.7956 (mmm) REVERT: A 3418 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8774 (p0) REVERT: A 3540 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.5765 (t80) REVERT: A 3586 LYS cc_start: 0.8793 (tptp) cc_final: 0.8525 (mmmt) REVERT: A 3613 MET cc_start: 0.9133 (tmm) cc_final: 0.8749 (ttp) REVERT: A 3856 MET cc_start: 0.7806 (tpt) cc_final: 0.7524 (tpt) REVERT: A 4109 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7882 (t0) REVERT: A 4122 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8798 (pt0) REVERT: D 34 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7697 (ptp90) REVERT: D 69 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: E 129 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8593 (ttpp) REVERT: E 167 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7381 (mpt) REVERT: E 409 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.6775 (t80) REVERT: F 137 ASP cc_start: 0.7408 (t0) cc_final: 0.7152 (t0) REVERT: F 223 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: F 225 TYR cc_start: 0.8053 (m-80) cc_final: 0.7471 (m-80) REVERT: F 461 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8482 (mtm) outliers start: 202 outliers final: 143 residues processed: 668 average time/residue: 0.2105 time to fit residues: 239.9739 Evaluate side-chains 652 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 490 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1202 ARG Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1711 ARG Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1992 VAL Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2408 MET Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2429 ASP Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2486 ASP Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3456 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3614 TYR Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 607 PHE Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 9 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 442 optimal weight: 4.9990 chunk 382 optimal weight: 0.9980 chunk 225 optimal weight: 0.0770 chunk 489 optimal weight: 20.0000 chunk 350 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN A1049 GLN A1084 ASN A1325 GLN A2859 GLN A2977 ASN A4000 ASN A4088 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099809 restraints weight = 83374.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101079 restraints weight = 45896.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101759 restraints weight = 31370.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102190 restraints weight = 30293.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102274 restraints weight = 26828.888| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41708 Z= 0.136 Angle : 0.655 13.665 56668 Z= 0.326 Chirality : 0.041 0.180 6390 Planarity : 0.004 0.071 6926 Dihedral : 14.247 176.025 6143 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.55 % Favored : 90.41 % Rotamer: Outliers : 4.55 % Allowed : 28.71 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.13), residues: 4818 helix: 0.98 (0.11), residues: 2661 sheet: -1.32 (0.36), residues: 204 loop : -2.17 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3612 TYR 0.017 0.001 TYR F 416 PHE 0.032 0.001 PHE A2577 TRP 0.011 0.001 TRP A3916 HIS 0.005 0.001 HIS F 188 Details of bonding type rmsd covalent geometry : bond 0.00316 (41708) covalent geometry : angle 0.65489 (56668) hydrogen bonds : bond 0.03128 ( 1943) hydrogen bonds : angle 4.19622 ( 5541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 511 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 MET cc_start: 0.9105 (mpp) cc_final: 0.8649 (mpp) REVERT: A 441 MET cc_start: 0.7890 (tpp) cc_final: 0.7289 (tpp) REVERT: A 707 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 734 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8901 (mm) REVERT: A 831 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 1255 CYS cc_start: 0.8266 (m) cc_final: 0.7908 (m) REVERT: A 1269 THR cc_start: 0.9137 (t) cc_final: 0.8911 (t) REVERT: A 1561 SER cc_start: 0.8610 (m) cc_final: 0.8394 (p) REVERT: A 1648 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 1711 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: A 1724 MET cc_start: 0.7757 (mmm) cc_final: 0.7043 (mtp) REVERT: A 1946 ASN cc_start: 0.9417 (m-40) cc_final: 0.8861 (m110) REVERT: A 1967 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: A 2356 MET cc_start: 0.7497 (pmm) cc_final: 0.6456 (pmm) REVERT: A 2568 MET cc_start: 0.8394 (ppp) cc_final: 0.7794 (ppp) REVERT: A 2860 ASP cc_start: 0.8463 (t0) cc_final: 0.8095 (t0) REVERT: A 3232 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6753 (tmm-80) REVERT: A 3414 MET cc_start: 0.8218 (mmm) cc_final: 0.7958 (mmm) REVERT: A 3418 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8779 (p0) REVERT: A 3540 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.5707 (t80) REVERT: A 3613 MET cc_start: 0.9175 (tmm) cc_final: 0.8756 (ttp) REVERT: A 4109 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.7908 (t0) REVERT: A 4122 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8816 (pt0) REVERT: D 34 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7718 (ptp90) REVERT: D 69 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: E 129 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8612 (ttpp) REVERT: E 167 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7334 (mpt) REVERT: E 409 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.6748 (t80) REVERT: E 498 MET cc_start: 0.8018 (tpp) cc_final: 0.7778 (tpp) REVERT: F 223 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: F 461 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8409 (mtm) outliers start: 198 outliers final: 139 residues processed: 658 average time/residue: 0.2233 time to fit residues: 248.5196 Evaluate side-chains 643 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 486 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 959 TYR Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1202 ARG Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1711 ARG Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1967 PHE Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2272 VAL Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2486 ASP Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 2977 ASN Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3107 ILE Chi-restraints excluded: chain A residue 3140 GLU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3456 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3614 TYR Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3712 LEU Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 607 PHE Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 409 PHE Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 83 optimal weight: 0.6980 chunk 236 optimal weight: 0.9990 chunk 414 optimal weight: 0.9990 chunk 465 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 466 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 268 optimal weight: 0.0040 chunk 479 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1084 ASN A1325 GLN A1772 HIS A2859 GLN ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102438 restraints weight = 83840.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104028 restraints weight = 43077.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104298 restraints weight = 29996.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104767 restraints weight = 28973.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104802 restraints weight = 26141.730| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41708 Z= 0.122 Angle : 0.666 14.457 56668 Z= 0.329 Chirality : 0.041 0.220 6390 Planarity : 0.004 0.072 6926 Dihedral : 14.214 175.738 6143 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.22 % Favored : 90.74 % Rotamer: Outliers : 3.67 % Allowed : 29.33 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 4818 helix: 0.99 (0.11), residues: 2669 sheet: -1.35 (0.36), residues: 200 loop : -2.14 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3612 TYR 0.016 0.001 TYR F 416 PHE 0.033 0.001 PHE A2577 TRP 0.014 0.001 TRP A3916 HIS 0.006 0.001 HIS A3643 Details of bonding type rmsd covalent geometry : bond 0.00277 (41708) covalent geometry : angle 0.66582 (56668) hydrogen bonds : bond 0.03021 ( 1943) hydrogen bonds : angle 4.16285 ( 5541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 528 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.1891 (OUTLIER) cc_final: 0.0504 (mmp-170) REVERT: A 326 MET cc_start: 0.9117 (mpp) cc_final: 0.8861 (mpp) REVERT: A 707 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7984 (t80) REVERT: A 734 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 831 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8601 (mm) REVERT: A 1255 CYS cc_start: 0.8336 (m) cc_final: 0.7979 (m) REVERT: A 1269 THR cc_start: 0.9096 (t) cc_final: 0.8868 (t) REVERT: A 1428 ILE cc_start: 0.9314 (mm) cc_final: 0.9088 (mm) REVERT: A 1711 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7868 (ttm-80) REVERT: A 1873 TYR cc_start: 0.8649 (m-80) cc_final: 0.8071 (m-80) REVERT: A 1946 ASN cc_start: 0.9401 (m-40) cc_final: 0.8841 (m110) REVERT: A 1967 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: A 2568 MET cc_start: 0.8350 (ppp) cc_final: 0.7855 (ppp) REVERT: A 2860 ASP cc_start: 0.8477 (t0) cc_final: 0.8087 (t0) REVERT: A 3000 ASP cc_start: 0.8851 (t0) cc_final: 0.8393 (t0) REVERT: A 3181 ASP cc_start: 0.8380 (m-30) cc_final: 0.8163 (m-30) REVERT: A 3232 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6739 (tmm-80) REVERT: A 3414 MET cc_start: 0.8192 (mmm) cc_final: 0.7592 (mmm) REVERT: A 3418 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8782 (p0) REVERT: A 3540 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.5704 (t80) REVERT: A 3613 MET cc_start: 0.9127 (tmm) cc_final: 0.8898 (tmm) REVERT: A 4109 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7869 (t0) REVERT: A 4122 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8834 (pt0) REVERT: D 34 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7695 (ptp90) REVERT: D 69 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: E 129 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8624 (ttpp) REVERT: E 167 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7343 (mpt) REVERT: E 409 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.6505 (t80) REVERT: F 223 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: F 369 ASP cc_start: 0.8233 (p0) cc_final: 0.7812 (t0) REVERT: F 461 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8516 (mtm) outliers start: 160 outliers final: 123 residues processed: 645 average time/residue: 0.2341 time to fit residues: 255.9448 Evaluate side-chains 630 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 489 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1711 ARG Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1967 PHE Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2486 ASP Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2876 VAL Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3140 GLU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3456 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3614 TYR Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 37 optimal weight: 4.9990 chunk 364 optimal weight: 1.9990 chunk 97 optimal weight: 0.0070 chunk 329 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 294 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 299 optimal weight: 0.6980 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1084 ASN A1325 GLN ** A3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.141217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104735 restraints weight = 85936.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106877 restraints weight = 42425.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.107288 restraints weight = 28092.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107943 restraints weight = 26836.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107798 restraints weight = 23054.388| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41708 Z= 0.125 Angle : 0.674 14.826 56668 Z= 0.332 Chirality : 0.041 0.208 6390 Planarity : 0.004 0.071 6926 Dihedral : 14.200 175.810 6143 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.17 % Favored : 90.78 % Rotamer: Outliers : 3.67 % Allowed : 29.24 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.13), residues: 4818 helix: 1.03 (0.11), residues: 2659 sheet: -1.41 (0.35), residues: 207 loop : -2.13 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3612 TYR 0.017 0.001 TYR A 385 PHE 0.032 0.001 PHE A2577 TRP 0.062 0.001 TRP A2245 HIS 0.008 0.001 HIS A3643 Details of bonding type rmsd covalent geometry : bond 0.00288 (41708) covalent geometry : angle 0.67388 (56668) hydrogen bonds : bond 0.03018 ( 1943) hydrogen bonds : angle 4.15017 ( 5541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9636 Ramachandran restraints generated. 4818 Oldfield, 0 Emsley, 4818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 504 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.2123 (OUTLIER) cc_final: 0.0787 (mmp-170) REVERT: A 326 MET cc_start: 0.9155 (mpp) cc_final: 0.8869 (mpp) REVERT: A 707 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 734 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8884 (mm) REVERT: A 831 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8572 (mm) REVERT: A 1255 CYS cc_start: 0.8403 (m) cc_final: 0.8019 (m) REVERT: A 1269 THR cc_start: 0.9117 (t) cc_final: 0.8897 (t) REVERT: A 1428 ILE cc_start: 0.9323 (mm) cc_final: 0.9097 (mm) REVERT: A 1711 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7867 (ttm-80) REVERT: A 1724 MET cc_start: 0.7479 (mmm) cc_final: 0.6916 (mtp) REVERT: A 1873 TYR cc_start: 0.8664 (m-80) cc_final: 0.8075 (m-80) REVERT: A 1880 MET cc_start: 0.8233 (mmm) cc_final: 0.7886 (mmt) REVERT: A 1946 ASN cc_start: 0.9430 (m-40) cc_final: 0.8872 (m110) REVERT: A 1967 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: A 2236 GLU cc_start: 0.8956 (tt0) cc_final: 0.8417 (tp30) REVERT: A 2568 MET cc_start: 0.8395 (ppp) cc_final: 0.7924 (ppp) REVERT: A 2860 ASP cc_start: 0.8423 (t0) cc_final: 0.8041 (t0) REVERT: A 3000 ASP cc_start: 0.8979 (t0) cc_final: 0.8444 (t0) REVERT: A 3232 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6743 (tmm-80) REVERT: A 3414 MET cc_start: 0.8189 (mmm) cc_final: 0.7638 (mmm) REVERT: A 3418 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8777 (p0) REVERT: A 3540 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5709 (t80) REVERT: A 3586 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8215 (mmmt) REVERT: A 3613 MET cc_start: 0.9182 (tmm) cc_final: 0.8776 (ttp) REVERT: A 4109 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7919 (t0) REVERT: A 4122 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8800 (pt0) REVERT: D 34 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7726 (ptp90) REVERT: D 69 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: E 129 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8545 (ttpp) REVERT: E 167 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7433 (mpt) REVERT: E 409 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.6701 (t80) REVERT: E 498 MET cc_start: 0.8004 (tpp) cc_final: 0.7679 (tpp) REVERT: F 223 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: F 369 ASP cc_start: 0.8100 (p0) cc_final: 0.7727 (t0) REVERT: F 461 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8468 (mtm) outliers start: 160 outliers final: 127 residues processed: 622 average time/residue: 0.2182 time to fit residues: 230.4114 Evaluate side-chains 635 residues out of total 4354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 490 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 346 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 707 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1102 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1409 SER Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1479 VAL Chi-restraints excluded: chain A residue 1515 LEU Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1655 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1694 THR Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1711 ARG Chi-restraints excluded: chain A residue 1719 VAL Chi-restraints excluded: chain A residue 1741 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1813 SER Chi-restraints excluded: chain A residue 1858 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1933 LEU Chi-restraints excluded: chain A residue 1967 PHE Chi-restraints excluded: chain A residue 1988 TYR Chi-restraints excluded: chain A residue 2142 ILE Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2215 LEU Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2424 MET Chi-restraints excluded: chain A residue 2449 VAL Chi-restraints excluded: chain A residue 2468 THR Chi-restraints excluded: chain A residue 2486 ASP Chi-restraints excluded: chain A residue 2533 SER Chi-restraints excluded: chain A residue 2785 ILE Chi-restraints excluded: chain A residue 2791 ILE Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3063 THR Chi-restraints excluded: chain A residue 3078 LEU Chi-restraints excluded: chain A residue 3091 LEU Chi-restraints excluded: chain A residue 3123 GLN Chi-restraints excluded: chain A residue 3140 GLU Chi-restraints excluded: chain A residue 3145 ILE Chi-restraints excluded: chain A residue 3155 VAL Chi-restraints excluded: chain A residue 3232 ARG Chi-restraints excluded: chain A residue 3348 LEU Chi-restraints excluded: chain A residue 3418 ASP Chi-restraints excluded: chain A residue 3450 MET Chi-restraints excluded: chain A residue 3456 LEU Chi-restraints excluded: chain A residue 3490 VAL Chi-restraints excluded: chain A residue 3505 LEU Chi-restraints excluded: chain A residue 3516 HIS Chi-restraints excluded: chain A residue 3540 TYR Chi-restraints excluded: chain A residue 3614 TYR Chi-restraints excluded: chain A residue 3694 PHE Chi-restraints excluded: chain A residue 3701 ILE Chi-restraints excluded: chain A residue 3726 VAL Chi-restraints excluded: chain A residue 3792 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3803 ILE Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3907 SER Chi-restraints excluded: chain A residue 3974 MET Chi-restraints excluded: chain A residue 3997 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain A residue 4109 ASP Chi-restraints excluded: chain A residue 4122 GLU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 177 TRP Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 359 HIS Chi-restraints excluded: chain E residue 409 TYR Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 607 PHE Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain F residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 466 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 161 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 374 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 GLN A1084 ASN A1325 GLN A1772 HIS A2859 GLN A3634 GLN A4000 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103590 restraints weight = 86858.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105163 restraints weight = 42497.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105477 restraints weight = 29326.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105969 restraints weight = 29292.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106173 restraints weight = 25107.560| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41708 Z= 0.151 Angle : 0.683 14.539 56668 Z= 0.339 Chirality : 0.041 0.239 6390 Planarity : 0.004 0.070 6926 Dihedral : 14.246 176.029 6143 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.32 % Favored : 90.64 % Rotamer: Outliers : 3.81 % Allowed : 29.17 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.13), residues: 4818 helix: 1.01 (0.11), residues: 2664 sheet: -1.55 (0.35), residues: 207 loop : -2.14 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3612 TYR 0.021 0.001 TYR A 385 PHE 0.032 0.001 PHE A2577 TRP 0.049 0.001 TRP A2245 HIS 0.012 0.001 HIS A3643 Details of bonding type rmsd covalent geometry : bond 0.00356 (41708) covalent geometry : angle 0.68316 (56668) hydrogen bonds : bond 0.03159 ( 1943) hydrogen bonds : angle 4.18139 ( 5541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7564.37 seconds wall clock time: 131 minutes 20.82 seconds (7880.82 seconds total)